Criteria Specification Registry

Please note this is an alpha version of the Criteria Specification Registry. This resource is intended to provide access to Criteria Specifications used and applied by ClinGen Variant Curation Expert Panels and biocurators in the classification of variants.

For general information about ClinGen Expert Panels and Variant Curation please visit: Clinical Domain Working Groups. For specific inquiries regarding content correction or adding a new criteria specification refer to the Help page.

This resource is undergoing updates and tesing. Should you encounter any issues regarding the data displayed, lack of functionality or other problems, please let us know by contacting us via email so we can rectify these accordingly. Your help in this regard is greatly appreciated.

Help

Content Correction

To add a new criteria specification or change the content of a specification in the CSpec Registry:

Fill the Criteria Specification as mentioned in the template here.
Once filled, send the template to brl-cspec at bcm dot edu
The upcoming release of the Cspec Editor will allow VCEP coordinators and other members to directly add or change a Criteria Specification.

API Documentation - JSON

Introduction to CSPEC Web & API Services

The Criteria Specifiication Registry provides RESTful-APIs to browse and search content. Responses are returned in JSON format.

Service URL: https://cspec.genome.network/cspec/

API Endpoints

Several REST API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.

Endpoints	Description	Example
/srvc	CSpec Service; lists all entity types and counts	https://cspec.genome.network/cspec/srvc
/id/{val}	Non-specific identity-based lookup	https://cspec.genome.network/cspec/id/GN016
/{type}	Get info about an CSpec entity type	https://cspec.genome.network/cspec/SequenceVariantInterpretation
/{type}/id	Paged list; Batch entity retrieval	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id
/{type}/id/{val}	Specific identity-based lookup for an entity type	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016
/{type}/id/{val}/ld /{type}/id/{val}/ldFor	Get LD for an entity or get entities for which this one IS LD	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ld https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ldFor
/{type}/id/{val}/types /{type}/id/{val}/types/ld /{type}/id/{val}/types/ldFor	Get the list of types for an entity or get types of LD an entity has or types it is LD for; includes entity counts	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ld https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ldFor

API Modifiers

Response from the API endpoints can be filtered or restricted using the following modifiers:

Modifiers	Possible values	Description	Example
ids	Comma separated list of identifiers	Allows batch search of a list of identifiers	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015
types	Comma separated list of entity types	Allows filtering the results to show certain entity types only	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet
detail	low, med, high	low - Only identifier level info for the entity. The ld and ldFor just show the counts for 1+ such linked entity. med - (default) - The ld and ldFor show identifier level info. high - All details are shown.	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=med https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high
fields	Coming soon (Full list of fields will be added in a separate section.)	Comma separated list of fields to get in the API response	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId https://cspec.genome.network/cspec/CriteriaCode/id?detail=high&fields=entId,ldhId,entContent.label,entContent.strengthDescriptor
pg	Integer Default: 1 Min:1	Page number to be retrieved	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=1&pgSize=250&detail=low&fields=entId,ldhId
pgSize	Integer Default: 250 Min 1; Max: 250	Number of results in each page	https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=6&pgSize=250&detail=low&fields=entId

Key Fields in API Response

The table below lists the key fields returned in the API response.

Key Fields	Description	Example
ld	This entity is a linked data object for these entities	"ld": [ { "CriteriaCode": [ … ] }, {"RuleSet": [ … ] }, { "Gene": [ … ] } ], Here, "CriteriaCode", "RuleSet" and "Gene" are the linked data entities for the variant "CA000176"
ldFor	This entity is linked data FOR these other entities	"ldFor": [ { "Gene": [ … ] } ], SequenceVariantInterpretation “CA000176” is linked data FOR the Gene “TP53”
entId	Identifier of entity in the external data source	"entId": "GN016", where "GN016" - ClinGen Allele Registry identifier for “SequenceVariantInterpretation”
entIri	IRI of entity in the external data source	"entIri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097", where the IRI is the “link” to this entity in the external data source
entType	Type of entity	"entType": "SequenceVariantInterpretation",
ldhId	CSpec identifier (Note: If data is embedded within CSpec, this will be the only identifier)	"ldhId": "41889804",
ldhIri	CSpec IRI (Note: If data is embedded within CSpec, this will be the only IRI)	"ldhIri": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/41889804"
entContent	Excerpts from external data source	"entContent": {...} The excerpt content will be different for each entity type. Detailed documentation for the excerpt content stored for each type of entity will be added soon.
modifier	Person who added this entity to CSpec	"modifier": "johndoe",
modified	Modification timestamp value	"modified": "2019-10-03T17:04:35.395Z",

API Documentation - JSON-LD

Introduction to CSPEC JSON-LD API Services

The Criteria Specifiication Registry provides RESTful JSON-LD APIs to browse and search content. Responses are returned in JSON-LD format. Listed below are examples of JSON-LD API endpoints.

Service URL: https://cspec.genome.network/cspec/

API Endpoints

Several REST JOSN-LD API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.

Endpoints	Description	Example
/api/context/{type}	Context to a specific entity type	https://cspec.genome.network/cspec/api/context/SequenceVariantInterpretation
/api/{type}/id/{val}	Specific JSON-LD based identity-based lookup for an entity type	https://cspec.genome.network/cspec/api/SequenceVariantInterpretation/id/GN016